In silico evaluation of the Eucalyptus transcriptome

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Eucalyptus ESTs corresponding to the protoporphyrinogen IX oxidase enzyme related to the synthesis of heme, chlorophyll, and to the action of herbicides

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Detecting Loci under Recent Positive Selection in Dairy and Beef Cattle by Combining Different Genome-Wide Scan Methods

As the methodologies available for the detection of positive selection from genomic data vary in terms of assumptions and execution, weak correlations are expected among them. However, if there is any given signal that is consistently supported across different methodologies, it is strong evidence that the locus has been under past selection. In this paper, a straightforward frequentist approach based on the Stouffer Method to combine P-values across different tests for evidence of recent positive selection in common variations, as well as strategies for extracting biological information from the detected signals, were described and applied to high density single nucleotide polymorphism (SNP) data generated from dairy and beef cattle (taurine and indicine). The ancestral Bovinae allele state of over 440,000 SNP is also reported. Using this combination of methods, highly significant (P<3.17×10-7) population-specific sweeps pointing out to candidate genes and pathways that may be involved in beef and dairy production were identified. The most significant signal was found in the Cornichon homolog 3 gene (CNIH3) in Brown Swiss (P = 3.82×10-12), and may be involved in the regulation of pre-ovulatory luteinizing hormone surge. Other putative pathways under selection are the glucolysis/gluconeogenesis, transcription machinery and chemokine/cytokine activity in Angus; calpain-calpastatin system and ribosome biogenesis in Brown Swiss; and gangliosides deposition in milk fat globules in Gyr. The composite method, combined with the strategies applied to retrieve functional information, may be a useful tool for surveying genome-wide selective sweeps and providing insights in to the source of selection.

Caracterização de uma região genômica relacionada a uma anomalia de viveiro em Eucalyptus

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Identificação e caracterização de possiveis marcadores moleculares em carcinoma renal de células claras

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genome-wide association study for feedlot average daily gain in Nellore cattle (Bos indicus)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Cattle-Derived Microsatellite Markers to Study the Water Buffalo Genome

Microsatellites are well-known DNA markers used in a variety of studies such as genome mapping, genetic diversity analysis, genetic conservation and phylogenetic studies. Although microsatellites are important markers, their development and characterization demands extensive time and high cost. Thus, before new markers are developed for a particular species, it is worthwhile to test the available markers from related species. In the present study, we evaluate cattle-derived microsatellite markers for genetic studies of water buffalo. Eighty-five percents of a total of 120 microsatellite markers were optimized using buffalo DNA (Bubalus bubalis). The results showed in this paper were also deposited in the National Center for Biological Information database (NCBI) (ProbeDB and UniSTS) for use in population genetic studies of buffalo by the scientific community. The use of heterologous primers significantly reduces the cost of developing specific markers for buffalo, providing a useful short cut for the genetic population analysis and gene mapping studies.

The Automatic Mapping of Princeton WordNet Lexical-Conceptual Relations onto the Brazilian Portuguese WordNet Database

Princeton WordNet (WN.Pr) lexical database has motivated efficient compilations of bulky relational lexicons since its inception in the 1980's. The EuroWordNet project, the first multilingual initiative built upon WN.Pr, opened up ways of building individual wordnets, and interrelating them by means of the so-called Inter-Lingual-Index, an unstructured list of the WN.Pr synsets. Other important initiative, relying on a slightly different method of building multilingual wordnets, is the MultiWordNet project, where the key strategy is building language specific wordnets keeping as much as possible of the semantic relations available in the WN.Pr. This paper, in particular, stresses that the additional advantage of using WN.Pr lexical database as a resource for building wordnets for other languages is to explore possibilities of implementing an automatic procedure to map the WN.Pr conceptual relations as hyponymy, co-hyponymy, troponymy, meronymy, cause, and entailment onto the lexical database of the wordnet under construction, a viable possibility, for those are language-independent relations that hold between lexicalized concepts, not between lexical units. Accordingly, combining methods from both initiatives, this paper presents the ongoing implementation of the WN.Br lexical database and the aforementioned automation procedure illustrated with a sample of the automatic encoding of the hyponymy and co-hyponymy relations.

A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs

The desert locust (Schistocerca gregaria) has been used as material for numerous cytogenetic studies. Its genome size is estimated to be 8.55 Gb of DNA comprised in 11 autosomes and the X chromosome. Its X0/XX sex chromosome determinism therefore results in females having 24 chromosomes whereas males have 23. Surprisingly, little is known about the DNA content of this locust's huge chromosomes. Here, we use the Feulgen Image Analysis Densitometry and C-banding techniques to respectively estimate the DNA quantity and heterochromatin content of each chromosome. We also identify three satellite DNAs using both restriction endonucleases and next-generation sequencing. We then use fluorescent in situ hybridization to determine the chromosomal location of these satellite DNAs as well as that of six tandem repeat DNA gene families. The combination of the results obtained in this work allows distinguishing between the different chromosomes not only by size, but also by the kind of repetitive DNAs that they contain. The recent publication of the draft genome of the migratory locust (Locusta migratoria), the largest animal genome hitherto sequenced, invites for sequencing even larger genomes. S. gregaria is a pest that causes high economic losses. It is thus among the primary candidates for genome sequencing. But this species genome is about 50 % larger than that of L. migratoria, and although next-generation sequencing currently allows sequencing large genomes, sequencing it would mean a greater challenge. The chromosome sizes and markers provided here should not only help planning the sequencing project and guide the assembly but would also facilitate assigning assembled linkage groups to actual chromosomes.

Biomass burning fuel consumption rates: a field measurement database

Landscape fires show large variability in the amount of biomass or fuel consumed per unit area burned. Fuel consumption (FC) depends on the biomass available to burn and the fraction of the biomass that is actually combusted, and can be combined with estimates of area burned to assess emissions. While burned area can be detected from space and estimates are becoming more reliable due to improved algorithms and sensors, FC is usually modeled or taken selectively from the literature. We compiled the peerreviewed literature on FC for various biomes and fuel categories to understand FC and its variability better, and to provide a database that can be used to constrain biogeochemical models with fire modules. We compiled in total 77 studies covering 11 biomes including savanna (15 studies, average FC of 4.6 t DM (dry matter) ha 1 with a standard deviation of 2.2), tropical forest (n = 19, FC = 126 +/- 77), temperate forest (n = 12, FC = 58 +/- 72), boreal forest (n = 16, FC = 35 +/- 24), pasture (n = 4, FC = 28 +/- 9.3), shifting cultivation (n = 2, FC = 23, with a range of 4.0-43), crop residue (n = 4, FC = 6.5 +/- 9.0), chaparral (n = 3, FC = 27 +/- 19), tropical peatland (n = 4, FC = 314 +/- 196), boreal peatland (n = 2, FC = 42 [42-43]), and tundra (n = 1, FC = 40). Within biomes the regional variability in the number of measurements was sometimes large, with e. g. only three measurement locations in boreal Russia and 35 sites in North America. Substantial regional differences in FC were found within the defined biomes: for example, FC of temperate pine forests in the USA was 37% lower than Australian forests dominated by eucalypt trees. Besides showing the differences between biomes, FC estimates were also grouped into different fuel classes. Our results highlight the large variability in FC, not only between biomes but also within biomes and fuel classes. This implies that substantial uncertainties are associated with using biome-averaged values to represent FC for whole biomes. Comparing the compiled FC values with co-located Global Fire Emissions Database version 3 (GFED3) FC indicates that modeling studies that aim to represent variability in FC also within biomes, still require improvements as they have difficulty in representing the dynamics governing FC.